Notes

Import Exp data

Filter Exp data

Filter samples based on total read count

Fix sample names

Add lineage and metadata to Gold Standard Data

Limosilactobacillus fermentum in the theoretical composition was changed to Lactobacillus fermentum

## Error in dimnames(x) <- dn : 
##   length of 'dimnames' [1] not equal to array extent

Fix sample names from ‘-’

Merge exp data with GS

Filter Taxa for Gold Standard

These are the taxa that were found in the experimental data

##                         species taxid superkingdom         phylum
## 1             Bacillus subtilis  1423     Bacteria     Firmicutes
## 2         Enterococcus faecalis  1351     Bacteria     Firmicutes
## 3              Escherichia coli   562     Bacteria Proteobacteria
## 4 Limosilactobacillus fermentum  1613     Bacteria     Firmicutes
## 5        Listeria monocytogenes  1639     Bacteria     Firmicutes
## 6        Pseudomonas aeruginosa   287     Bacteria Proteobacteria
## 7           Salmonella enterica 28901     Bacteria Proteobacteria
## 8         Staphylococcus aureus  1280     Bacteria     Firmicutes
##                 class            order             family               genus
## 1             Bacilli       Bacillales        Bacillaceae            Bacillus
## 2             Bacilli  Lactobacillales    Enterococcaceae        Enterococcus
## 3 Gammaproteobacteria Enterobacterales Enterobacteriaceae         Escherichia
## 4             Bacilli  Lactobacillales   Lactobacillaceae Limosilactobacillus
## 5             Bacilli       Bacillales       Listeriaceae            Listeria
## 6 Gammaproteobacteria  Pseudomonadales   Pseudomonadaceae         Pseudomonas
## 7 Gammaproteobacteria Enterobacterales Enterobacteriaceae          Salmonella
## 8             Bacilli       Bacillales  Staphylococcaceae      Staphylococcus
##     count Gram Stain   EXP_sum
## 1 1740000          + 1696.4170
## 2  990000          +  845.0235
## 3 1010000          - 3888.5896
## 4 1840000          +  956.4267
## 5 1410000          +  696.8151
## 6  420000          -  100.1231
## 7 1040000          -  409.6689
## 8 1550000          +  792.1799

Add Gram Stain Info

Omit Eukaryotes

Homo sapiens: Relative abundance of taxa at each taxonomic level

Gram Stain level

Phylum level

Class level

Order level

Family level

Genus level

Species level

Figure XB – no eval

Statistics

Phylum level

Heatmap of VST-normalized abundance values

Significant Differences - Statistics

##    is.significant     N
##            <lgcl> <int>
## 1:           TRUE     3
## 2:          FALSE    24

Significant Differences - Heatmap of log2FC values

Significant Differences - Heatmap of VST-normalized Abundance Values

Significant Differences - Heatmap of VST-normalized Abundance Differences

PERMANOVA

Full-model PERMANOVA: source + dna.isolation.method

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
##          Df SumOfSqs     R2      F Pr(>F)
## primer    2 0.073145 0.2651 1.0822  0.407
## Residual  6 0.202775 0.7349              
## Total     8 0.275920 1.0000

Order level

Heatmap of VST-normalized abundance values

Significant Differences - Statistics

##    is.significant     N
##            <lgcl> <int>
## 1:           TRUE    15
## 2:          FALSE    66

Significant Differences - Heatmap of log2FC values

Significant Differences - Heatmap of VST-normalized Abundance Values

Significant Differences - Heatmap of VST-normalized Abundance Differences

PERMANOVA

Full-model PERMANOVA: source + dna.isolation.method

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
##          Df SumOfSqs      R2      F Pr(>F)
## primer    2 0.075489 0.26976 1.1082  0.409
## Residual  6 0.204348 0.73024              
## Total     8 0.279837 1.00000

Genus level

Heatmap of VST-normalized abundance values

Significant Differences - Statistics

##    is.significant     N
##            <lgcl> <int>
## 1:           TRUE    63
## 2:          FALSE   441

Significant Differences - Heatmap of log2FC values

Significant Differences - Heatmap of VST-normalized Abundance Values

Significant Differences - Heatmap of VST-normalized Abundance Differences

PERMANOVA

Full-model PERMANOVA: source + dna.isolation.method

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
##          Df SumOfSqs      R2      F Pr(>F)
## primer    2 0.076531 0.27168 1.1191  0.396
## Residual  6 0.205161 0.72832              
## Total     8 0.281691 1.00000

Species level

Heatmap of VST-normalized abundance values

Significant Differences - Statistics

##    is.significant     N
##            <lgcl> <int>
## 1:          FALSE   910
## 2:           TRUE   165
## 3:             NA     5

Significant Differences - Heatmap of log2FC values

Significant Differences - Heatmap of VST-normalized Abundance Values

Significant Differences - Heatmap of VST-normalized Abundance Differences

PERMANOVA

Full-model PERMANOVA: source + dna.isolation.method

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
##          Df SumOfSqs      R2      F Pr(>F)
## primer    2 0.077607 0.27403 1.1324  0.384
## Residual  6 0.205601 0.72597              
## Total     8 0.283209 1.00000